Doctorant : Aurélie Deroy
Université : Université de Lorraine, France
Durée du contrat : 2012-2015
Titre de la thèse — Connecting genomic polymorphism and phenomic variability in fungal wood decayers
Equipe d’accueil et encadrant(s) —
Research teams : IAM (Stress response and redox regulation)/ LERMAB
PhD supervisor : P. Gérardin (LERMAB)/E. Gelhaye (IAM)/M. Morel-Rouhier (IAM)
Contexte et état de l’art —
Saprotrophic Agaricomycotina are of particular interest as they are active and abundant degraders of all classes of plant tissues. Among them, wood-decaying fungi can be divided into two main groups, brown and white rot, depending on their ability to degrade/mineralize lignin. The brown-rot fungi are able to modify lignin to gain access to the cellulose and hemicelluloses. The recent release of genomes of Postia placenta and Serpula lacrymans has for instance allowed the confirmation of previous biochemical works that demonstrate that this step is mainly mediated by non-enzymatic reactions. Briefly, brown-rot fungi use small phenolic compounds to reduce iron and produce hydrogen peroxide, prerequisite steps for the formation of hydroxyl radicals via the Fenton reaction. These radicals are involved in the lignin modification and in polysaccharides degradation. In contrast, the white-rot fungi are able to mineralize lignin, the oxidative degradation of this polymer being mainly mediated by the production of various oxidases and peroxidases, as the polysaccharides are largely degraded by a hydrolytic process mediated by glycosyl hydrolases. Besides the development of these complex extracellular enzymatic networks (Cazymes/Folymes) involved in wood degradation, wood decayers have also developed, as other organisms, a complex detoxification network called xenome. As in other organisms, the detoxification pathways against recalcitrant/toxic compounds can be divided in three different steps in fungi, the first one corresponding to an activation of the molecule (in particular cytochrome P450 monooxigenases), the second one to a conjugation stage (in particular glutathione transferases) and the third one to a transport/storage stage.
The fungal wood decayers exhibit indeed great variability within both their extracellular degradation and intracellular detoxification networks composed of multigenic families, which are largely extended in comparison to fungi belonging to other functional groups. This variability has been in particular described through comparative genomic approaches, however functional studies remain necessary to describe in detail the involvement of these various enzymes in plant cell wall decomposition and/or catabolism.
Objectifs et questions de recherche —
The main hypothesis supported by this work is that wood chemical composition is likely a major governing factor in the adaptation of these fungi to the diversity of their substrate and in particular, the rapid evolution of these networks.
Enjeux scientifiques et socio-économiques —
Plant cell walls are a potentially highly renewable resource for the production of biofuels. Complex raw materials from different origins (dedicated crops, agricultural wastes, etc.) constitute new potential sources of sugars that can be fermented for production of 2nd generation bioethanol. Another key-point is the valorization of by-products of biorefinery, such as phenolic compounds and lignin. Fungi and in particular polyporales are an extraordinary resource for identifying novel enzymes or synergistic factors that contribute to efficient biomass degradation or transformation. In particular, oxidative enzymes are increasingly studied for their key role in the enzymatic mechanisms developed by Basidiomycetes to degrade lignocellulose. Such oxidative enzymes are used to complement commercial enzymatic cocktails originated from the industrial fungal work-horses (Ascomycetes fungi A. niger and T. reesei). The integrative analysis of genomics, transcriptomics and enzymatic functionalities will provide an efficient mean to identify the key enzymes involved in plant cell wall deconstruction.
Approches méthodologiques et résultats attendus —
We choose to study the saprobe Trametes versicolor, a fungus easily found in forest ecosystems and also largely used as the reference fungus when testing the efficacy of wood preservatives, mainly on hardwood species (beech), in accordance with European standards of wood preservation tests. This choice also corresponds with a more long-term objective which is to understand how the chemical composition of wood infers on its susceptibility to biological attack. This project dealing with the connection of genetic variations to phenotypic variations is sustained by the complementary expertise of the different partners allowing exploration at the molecular level of environmental factors governing local fungal adaptation and developing possible applications for biorefinery and white biotechnology.